Oxygen depletion in the upper ocean is commonly associated with poor ventilation and storage of respired carbon, potentially linked to atmospheric CO2 levels. Iodine to calcium ratios (I/Ca) in recent planktonic foraminifera suggest that values less than ~2.5 μmol mol−1 indicate the presence of O2-depleted water. Here we apply this proxy to estimate past dissolved oxygen concentrations in the near surface waters of the currently well-oxygenated Southern Ocean, which played a critical role in carbon sequestration during glacial times. A down-core planktonic I/Ca record from south of the Antarctic Polar Front (APF) suggests that minimum O2 concentrations in the upper ocean fell below 70 μmol kg−1 during the last two glacial periods, indicating persistent glacial O2 depletion at the heart of the carbon engine of the Earth’s climate system. These new estimates of past ocean oxygenation variability may assist in resolving mechanisms responsible for the much-debated ice-age atmospheric CO2 decline.